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Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Trifolium repens in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U7P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.2 M ammonium dihydrogen orthophosphate, 15% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.96 37.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.83 α = 90 b = 51.91 β = 108.46 c = 69.46 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2009-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.15 65.9 100 0.136 6.2 3.6 19997 32.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5u7p 2.15 35.43 18952 1030 99.93 0.19912 0.19544 0.1993 0.26451 0.2669 RANDOM 34.075
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.502 r_dihedral_angle_4_deg 20.16 r_dihedral_angle_3_deg 16.672 r_dihedral_angle_1_deg 7.088 r_long_range_B_refined 6.305 r_long_range_B_other 6.305 r_scangle_other 4.116 r_mcangle_it 3.632 r_mcangle_other 3.631 r_scbond_it 2.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.502 r_dihedral_angle_4_deg 20.16 r_dihedral_angle_3_deg 16.672 r_dihedral_angle_1_deg 7.088 r_long_range_B_refined 6.305 r_long_range_B_other 6.305 r_scangle_other 4.116 r_mcangle_it 3.632 r_mcangle_other 3.631 r_scbond_it 2.696 r_scbond_other 2.695 r_mcbond_other 2.475 r_mcbond_it 2.474 r_angle_refined_deg 1.763 r_angle_other_deg 0.83 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2987 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing